theislab/single-cell-best-practices resource

Health v2 · maintenance only

Flags: no_license

Adoption not part of the score

1253 stars · 277 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

An open-source Jupyter book teaching best practices for single-cell RNA-seq and multi-modal single-cell analysis, accompanying a Nature Reviews Genetics expert recommendation. It provides executable notebooks with Conda environments covering the full single-cell analysis workflow.

Use cases

• learn single-cell RNA-seq analysis best practices
• tutorial for analyzing scRNA-seq data with Python
• how to preprocess and quality-control single-cell data
• guide for multi-modal single-cell analysis workflows
• reproducible notebooks for single-cell genomics
• learn Scanpy-based single-cell analysis

When to choose

• you are a beginner or analyst learning single-cell analysis end to end
• you want executable, reproducible notebooks with recommended tools
• you need a citable, community-reviewed reference for single-cell workflows

When to avoid

• you need production software rather than teaching material
• you require R-only workflows (the book is primarily Python-based)
• you need a maintained tool with guaranteed long-term support - the project is actively seeking maintainers

Facets

learning-resource · maturity active

documentation data-science machine-learning bioinformatics tutorials education python jvm jupyter-book single-cell-rna-seq genomics scanpy bioinformatics-tutorial

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